All Alone in the Night
by Hoosier87
Summary: Commander Chamberlain was one of the best commandos in the Alliance. Then he was given orders that would change his life. Rate M for strong language, violence, and sexual themes/scenes
1. Prologue: SR2

Author's Note: This is the first story I've posted in a long time. I really love Mass Effect, and I hope this story does it justice. The plotline will run along the end of Mass Effect, and then move into the time after the game. It will follow an original character, who will be introduced in the next chapter.

Disclaimer: Mass Effect is owned by Bioware and Microsoft.

A long oaken table sat in the center of a long room. The walls were crafted of steel dulled by time, cold and uninviting, and the atmosphere of the room was not helped by the sterile lighting. And being several stories underground did not help ease the claustrophobia. A lone figure, an Alliance Fleet steward, entered through a pair of doors on the right side of the room and went to each of the half-dozen seats around the table placing a small datapad with a dossier on it. The young solider left the room, but returned a few moments later with two pitchers of water. He placed them carefully on the table, and then followed suit the glasses he retrieved. His work finished the solider left the room. Silence hung across the room.

The still scene was shattered as the doors opened a dozen men with the golden bars of an admiral. Seated at the head of the table was Fleet Admiral Michael Swenson. A lean man with hawkish features and salt-and-pepper hair, Fleet Admiral Swenson, who was pushing 87, was the Chairman of the Joint Chiefs. Many first meeting Swenson were fooled by his age, believing him to be nearing retirement. Most fleet personnel retired around 90 to enjoy their last 40 or so years of life. Swenson was not going to sit idly by and let others run the military. It was still his operation, with power delegated to him directly from President Jeruta. Swenson smiled and sat, motioning for the other admirals to do the same.

"Admiral Hackett," Fleet Admiral Swenson said, words reverberating off the steel walls for the first time that day, "welcome to Washington. I hope your trip from Arcturus Prime wasn't too taxing."

Hackett nodded. "It was a normal trip, no surprises, sir." As commander of the Fifth Fleet, the largest and most powerful in the Alliance Fleet, Hackett spent much of his time on Arcturus Station. The Alliance had very publically claimed that Arcturus Station was the headquarters for all fleet operations. In one sense, it was true; in another, completely false.

Arcturus Station oversaw most of the day-to-day workings of the fleet: provisions, movement, training, patrol patterns, and such. The bulk of the bureaucracy was at Arcturus Station. The nerve center, the top brass, met in one of the sub-basements of the Pentagon in Washington D.C., North America. One of the lessons of the First Contact War was just how vulnerable a space-based commander center was. Taking this lesson, the Joint Chiefs relocated themselves back to Earth, safely behind the Planetary Defense System that ringed humanity's home-world.

Admiral Swenson nodded. "We've all had a chance to look over Rear Admiral Mikhailovich's report on SR-1, SSV Normandy. Opinions?" he asked of his assembled advisors.

Admiral Gillett, Chief of Ordinance, spoke up first. "Sir, I agree with Mikhailovich," he stated calmly in his French accent, "Normandy is a fine machine, but she costs simply too much money. We can use ze taxpayer's dollars more effectively on proven weapons."

Admiral Zhan, Chief of Intelligence, countered. "Any new weapon is expensive. Commander Shepard is right," Zhan said emphatically, gesturing to the datapad, "that stealth system will be invaluable in intelligence gathering and planning. Sir, the insight and tactical data gathered could save thousands of lives and dozens of ships by giving them solid, up to date intelligence."

As Zhan finished, the room descended into chaos as each admiral sought to make his opinion heard. Admiral Swenson let the noise continue for a few moments, and the raised his hand, silencing the room. All heads turned to face the head of the table.

Admiral Swenson looked right at Admiral Hackett. "Admiral, you know Normandy's record better than any of us. What is your opinion?"

Admiral Hackett, seated at the foot of the table, leaned forward, resting his forehead against his hands. After a few moments, he spoke up. "Sir, I think Normandy has performed wonderfully. I have been able to entrust several highly sensitive assignments to Commander Shepard, such as the old espionage probe in the Amazon System or the recovery of the data module that was shot down by geth in the Hercules System, and know that they would be accomplished. Sir, a vessel like Normandy needs a superb skipper to get her full abilities out. Sir, Normandy-class vessels are not a waste of money. They are powerful, fast, and quiet."

Admiral Swenson nodded. "Would you recommend the production of another Normandy-class ship?"

Hackett paused, clearly weighing his words, and then nodded firmly. "Yes sir. Another ship like that would dramatically increase our scouting and long range capabilities, and would give us the opportunity to further out relationship with the Citadel Fleet."

Swenson nodded. "I agree." He picked up his datapad, scribbled a few orders on it, and handed it to a steward he had just summoned to the room. The steward saluted and left the room.

"Gentlemen," Swenson announced, "I have just order the construction of SR-2, SSV Guadalcanal."


	2. Chapter 1: Rolling With Thunderstorms

The engine hummed

The engine hummed in a steady and constant frequency. The closer to aft you got on the frigate; the more pronounced the sound was. Commander Logan Chamberlain sat in the garage area of SSV Gettysburg, a frigate class vessel, tending to his pistol, a Karpov VII from Rosenkov Materials. He leaned back against the cold steel, oiling the dull blue metal of his weapon. Beside him sat his sniper rifle, a Punisher VII from Armax Arsenal. The dark blue and black color scheme of the metal glinted in the fluorescent light of the garage.

A voice called out, "Yo, Gan!"

Logan looked up and smiled for a moment, his deep brown eyes twinkling, as Sergeant Justin Simone got off the elevator. Simone was a big bull of a man who loved guns, cigars, beer, and women. Basically, he was the perfect sergeant.

"You still working on your guns? Didn't you clean those an hour ago?" Logan smiled and wordlessly nodded to a paint covered target at the far end of the garage. "Oh," Simone said sheepishly, an embarrassed flush clearly evident on his black skin.

"You need anything Justin?" Logan asked, speaking up for the first time.

"Yeah, just wanted to let you know that those news vids you were looking for just got in." Simone told him.

Logan nodded. "Thanks Justin."

Simone laughed and gave his friend an affectionate punch in the shoulder. "It's all good. Chow's in 5." Simone stepped back into the elevator and headed back to the mess hall on the deck above.

Rubbing his shoulder slightly and chuckling to himself, Logan crossed the garage where a small table had been set up with a vid-player. He brought up the screen, selected news and played the first vid.

"Exo-Geni reported today that it's colony on Feros has begun to turn a profit…"

Logan skipped to the next vid.

"Administrator Anoleis, head of the research facility on Noveria, was arrested recently. On an unrelated note, an industrial accident on the Peak 15 facility…"

Logan skipped to the next vid. Some report on a production of _Hamlet_ with Elcor. Next vid. Another recruiting effort with one of those "Profiles in Courage." Logan sighed. He wasn't going to get much more substantive news. He flipped the switch and stowed the viewer in its secure holder. Crossing back to his little nook in the wall, Logan grabbed his pistol and sniper rifle. Holstering the pistol and slinging the rifle across his back, he summoned the elevator and rode it up.

The elevator doors slid open soundlessly. Logan stepped out and crossed to a row of lockers. Dropping to one knee, he opened the locker and put his rifle and pistol in, and promptly closed it. When he stood, he was face-to-face with a blonde woman standing about 5'7 with striking blue eyes. Logan smiled. "Whitney, what do you want?" he asked coyly.

Lieutenant Whitney Chalker gave a pouty look. "Is that any way to greet your second?"

Logan smiled a wide and playful grin. "It is when she sneaks up on you."

Whitney laughed a musical little laugh. "Where have you been? I've not seen you all day."

Logan shrugged. "I was in the garage: weapon maintenance, target practice, cleaning, and then watching the news vids, that kind of stuff."

Whitney playfully nudged Logan's shoulder. "You work to hard. You should relax more."

Logan's eyebrows shot up. "Well Lieutenant, do you have any suggestions?" he asked, one of his arms sliding surreptitiously around her waist.

With a sly wink, Whitney slid out of the half-embrace. "I have some ideas, but," she leaned in and whispered salaciously in his ear, "you're gonna have to wait until we're off duty to find out what they are." With that, she turned and walked away, intentionally swinging her hips to tease Logan.

Chuckling softly to himself and shaking his head, Logan grabbed a tray and, after reaching the mess line, moved down it. He walked to the giant table in the center of the room with a chicken breast with rice and broccoli on his tray and sat down. He closed his eyes and bowed his head silently in prayer. He stayed like this for a few minutes as the rest of the off-duty crew filtered in and each took his or her own food. Logan opened his eyes, took a forkful of rice and began to eat.

Justin sat down next to Logan, his plate piled high with beef and potatoes and a cold beer in his hand.

Logan raised his eyebrows, "Should you be drinking?"

Justin took a swig, "It's only one beer. Besides, I ain't on duty til morning."

Logan chuckled and took a bit of his chicken.

"Why are you eating that sissy food anyway? I always thought you were a tough son of a bitch," Justin teased.

"What, just because someone doesn't try to eat a whole cow at one sitting means they're not tough?" Whitney asked sharply as she sat down across from Logan, her plate filled to the brim with a salad.

Justin flushed. "Uh, no ma'm, that's not…" he stammered.

Logan laughed. "Relax Justin, she's just teasing you."

Whitney nodded. "Yep. Your disgusting eating habits are just part of your charm."

Justin rolled his eyes at the obvious dig and forked a potato into his mouth.

Before Logan was halfway through his dinner, a blaring alarm rang throughout the ship. The instant the call to general quarters was made; the mess became a maelstrom of activity. The cooks turned off the artificial heaters and stowed the food, gathered the trays, plates, and silverware, securely locking them in cabinets. The crewmen who had been eating bolted out of the mess hall like rabbits, scurrying up or down various stairwells to reach their posts. Logan sprinted up the stairs onto the bridge and skidded to a halt near Captain Diaz. Logan snapped a salute to his superior officer. "What's the status, ma'm?"

Captain Emma Diaz was short Latina woman, only 5'4, yet she carried herself as if she were seven feet tall. Her hair, which undone would hang to her shoulders, was pulled back in a ponytail. In the light of the C&C (Command and Control), the faint grey streaks in her hair were visible. Diaz smiled at her second-in-command. "At ease Commander. We've got an unknown vessel approaching out of the terminus systems."

"Raiders?" Logan asked, he stomach clenching. He remembered the atrocities committed by raiders during the Alliance campaigns against the Terminus pirates.

"Unknown," was Diaz's reply, "But I want your team ready, just in case.

Logan nodded in agreement. "How long until contact?"

Diaz glanced at the screen in front of her. "5 minutes. Dismissed, Commander."

Logan saluted. "Yes ma'm." He turned on his and headed below deck to where the lockers were stowed. Justin and Whitney were already there putting on armor and adjusting weapons.

"What's the situation Commander?" Justin asked all business.

Whitney, who was making sure her Savant V biotic amp was in place, turned her head to listen.

"We've got an unidentified craft on an approach vector. Could be raiders. Captain wants us ready to go in case things turn ugly."

Justin grinned toothily and shouldered his shotgun. "Here's hoping they do. I'm feeling frisky."

Whitney and Logan stared at one another, and then burst out laughing. Justin blinked in confusion. "What?"

The two only laughed harder.

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"What the fuck is that!?" exclaimed the ruffled, and slightly hung-over, captain of the transport, MSV Thunderstorm.

"Looks to be a warship, probably an Alliance frigate…" the helmsman replied.

"What the hell is the Alliance doing in the Horsehead Nebula?" demanded the captain.

"Patrolling, I'd say, since it is under their jurisdiction. You know, with Noveria and other colonies nearby," the first mate responded.

"Fuck!" the captain exclaimed under this breath. "Get us out of here. Now."

"Sir, if we run…" the helmsman replied hesitantly.

"Just do it you fucker!" the captain shouted.

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"Ma'm, we have a confirmation on the ship's id," the helmsman said.

A few seconds of silence. "Well corporal, what is it?" Diaz demanded.

"Yes ma'm. Registration shows her as the MSV Thunderstorm. She's chartered to run supplies between Noveria and Terra Nova," the startled young solider replied.

Diaz crossed her arms pensively. "They're going the wrong way…" she murmured. "Hail them corporal."

"Yes ma'm," the corporal replied. He quickly entered the frequencies into the computer and spoke.

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"MSV Thunderstorm this is SSV Gettysburg. MSV Thunderstorm this is SSV Gettysburg. Please respond," the radio crackled.

The helmsman looked at the captain. "Sir?" he asked.

The captain ran his hand through his ruffled hair, obviously frustrated. He shook his head. "Don't respond, don't say anything. Just get us the hell out of here," he said.

The helmsman powered up the engines. "Yes sir," he said, though the worry in his voice was clear.

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"Ma'm their engines are powering up. They're running," the helmsman reported.

"The hell they are. Sergeant, take out their engines," Diaz barked.

"Yes ma'm," the sergeant said. Looking into his targeting reticule, the sergeant aligned the ship's main mass accelerator along the Thunderstorm's engines. He pulled the trigger.

Two bright beams of light emerged from the front of the vessel, streaking toward the transport. They struck the engines dead on. There was flash of fire that dissipated instantly.

Diaz smiled. "Nice shot, sergeant."

The sergeant smiled back. "Thank you ma'm."

"Alright corporal, take us in for a little visit." Diaz activated the ship's communication system. "Commander Chamberlain, be ready to board."

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"WHY THE FUCK AREN'T WE MOVING!!" screamed the captain.

"They've shot out our engines sir," reported the first mate, looking up from the consol.

"Son of bitch!" swore the captain.

"Sir, they're on an approach vector. I think they're gonna board us…" the helmsman said nervously.

"Fuck!" swore the captain, again.

"Sir, what do we do?" asked the first mate.

The captain thought for a moment. "Get everyone to the entry way. We're gonna fight. We're not gonna be thrown on some damn moon. No fucking way." The captain looked at his crew, who nodded. The entire bridge emptied as the pirates made their way to the entry way.

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Logan secured his helmet and grabbed a hold of the hand-hole. Justin was in front of the group, while Whitney was in the back. "Alright guys, you know the drill: standard boarding procedures. We encounter significant resistance, Whitney throws down a singularity. Justin, you're first." Ship jostled as the two airlocks connected. "Here we go," Logan said as his pistol left its holster.

The door hissed and slid open and the three were met by a hail a bullets. Quickly pressing their bodies against the steel wall as the bullets whizzed pass. Logan nodded to Whitney. Exposing her body briefly, she activated her biotic-amp and created her singularity.

Logan nodded and leaned out from behind the doorframe, firing his pistol into the spinning mass of bodies. With a wide grin, Justin did the same, his assault rifle chattering as it flung dozens of mass accelerated projectiles into the pirates.

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The captain stood in the doorway behind the entrance way watching in horror as his crew was shot to pieces, trapped helplessly in a mass effect field. His mouth hung open as the cries of his crew filled the large hold, their body's pierced time and again. Blood seeped from the trapped bodies and was also trapped in the spinning field. Finally, the bodies fell in a jumbled mass onto the floor. Turning, the captain ran further back into the ship.

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"Hold your fire!" Logan called out, his hand up. The guns fell silent. Nodding, the three soldiers crept into the hold. They moved silently through the hole-ridden bodies. Logan had numbed himself long ago to the sights and smells of battle, yet it still gripped at the stomach. Pressing his back to a crate, his eye caught a glimpse of the corpses, strewn carelessly among the blood, guts, and brain matter that stained the entry way. Saying a short prayer for the dead souls, he motioned his team forward.

They entered a narrow hallway. Logan and Justin stood shoulder to shoulder, while Whitney brought up the rear. Logan's hand shot up as they heard a door hiss shut to their immediate left. With a nod, they went down the short hallway to the compartment. Justin tried the door. It was locked. Logan leaned and activated his omni-tool, hacking into the computerized locking mechanism. He grinned as he received a satisfying ding and the door slid open. Logan pressed himself against the doorframe. Justin unlocked his shotgun, but Logan shook his head. "We need to take him alive, if possible," he told Justin, who nodded.

Logan peeked out, and immediately pistol rounds flew through the opening, several bouncing off of his kinetic shielding. Logan looked at Justin. "Well, I guess he's not going to surrender."

Justin's laughed a hearty guffaw at the joke.

"Give me some covering fired," Logan ordered.

Justin nodded and began firing into the room, forcing the pirate captain to take cover.

Logan made some minor calculations, and tightened his muscles, preparing to move, and then pressed two buttons on his omni-tool.

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"_Why aren't they coming in,_" wondered the captain as he fired his pistol into the doorway. "_They've killed everyone else so efficiently, why not just rush me. This is unnerving…_" Suddenly, his pistol overheated and wouldn't fire. The captain swore and scrambled around, looking for his spare pistol. He never found it.

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As soon as the sabotage hack went off, Logan sprang from the door like a tiger. He hurdled over an upturned table and, coming to a halt by the back wall, fired a single, well-aimed shot into the captain's forehead.

The pirate's head snapped back from the force of the shot. His shielding was down, so the single shot was fatal. A hole appeared in the back of his skull, spraying the back wall with blood and brains. The captain's eyes rolled back in his head as he crumpled over. The body hit the floor with a dull thud.

Logan holstered his pistol and began to search the room for anything useful. Justin and Whitney entered. Justin began to help Logan search. Whitney stared at the body.

"Was that necessary?" she asked slowly, pointing at the body.

Logan looked up from a desk on the right wall. "He wasn't going to surrender. He shot as soon as the door opened. Both times. It's a shame, but it couldn't be helped." The computer on the desk dinged. "Holy shit," Logan breathed "Captain Diaz is going to want to see this."

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Still in his armor, Logan approached Captain Diaz on the bridge of Gettysburg. "Captain, this is…well…" Logan stammered, unable to find the words, as he handed an OSD to Captain Diaz.

She nodded. "Good job Commander. Dismissed."

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Logan flopped onto his bed. He'd already peeled his armor off and stowed it in his locker with his weapons. He sighed and rubbed his temples, trying to tame the pulsing in his forehead. Sliding off of his back and onto his knees, he began to silently pray.

_Heavenly father, forgive me for the deaths I caused this day. Have mercy on the souls of those men and women who stand before you tonight. Keep this ship and her crew safe in our endeavors as we stand between the darkness and your children. This is all I ask of you. _

_Our father, who art in heaven,_

_Hallowed be thy name,_

_Thy kingdom come,_

_Thy will be done on Earth as in Heaven,_

_Give us this day our daily bread_

_Forgive our trespasses s we forgive those who trespass against us_

_And lead us not into temptation_

_But deliver us from evil_

_For thine is the kingdom and the power and the glory, for ever and ever._

As Logan was finishing, Whitney crept into his room. She smiled a little and, after he'd raised his head, she leaned in and softly kissed his neck. He smiled. "Hello to you too." Logan tilted his back slightly and kissed her softly, her tongue parting his lips.

Whitney guided Logan onto the bed and crawled on top of him. She broke the kiss and ran the back of her hand along Logan's cheek. "Well, I think it's time to help you relax," she said with a sultry smile. With a chuckle, she kissed him again, her hand sliding down to his groin. She gently massaged him, causing a low groan to emerge. Whitney laughed and kneeled back, straddling him and working down the button of her shirt and revealing her alabaster shoulder.

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Justin walked by the door to Logan's room. A long, low female moan managed to pierce the door. Justin broke into a wide grin and laugh. "Those two," he muttered to himself, highly amused. Justin shook his head, "Have fun. You guys deserve it." Justin turned and headed to his own bunk.

Captain Diaz put the OSD in the drive and pulled up the files. Her eyes moved from left to right across the screen, widening in shock and disbelief. "Sergeant, ensure that cargo in the Thunderstorm is secure in our hold. Corporal, set in a course for the Citadel and get my in touch with Ambassador Udina. The Council is going to want to see this."

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Author's note: I hope this is a satisfactory first chapter to follow the prologue. I will do my best to update regularly, hopefully once a week, but I satart working on monday, so no promises. Thanks for reading and I hope you enjoy this story!


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